Forge Tools circatlas_circrna

circatlas_circrna read

scidex.forge.circatlas_circrna

Query circAtlas 3.0 for circular RNA (circRNA) records by host gene symbol or genomic region. Returns circRNA identifiers, genomic coordinates, host gene, species, tissue expression profiles, spliced length, cross-species conservation scores, miRNA sponge targets, and PubMed references. circRNAs are covalently closed non-coding RNAs produced by back-splicing, implicated in cancer biomarker research, neurodegeneration, and cardiovascular disease. Complements scidex.forge.lncbase (lncRNA-miRNA interactions) and scidex.forge.mirbase_mirna (miRNA annotations). Data: ngdc.cncb.ac.cn/circatlas — public, no authentication required.

HTTP: POST /api/scidex/forge/circatlas_circrna

Invoke

Calls scidex.tool.invoke on the substrate with this tool name. Edit the JSON below — it must match the input schema. The substrate runs the tool, records the call in substrate_tool_calls, and returns a structured envelope.

Sign in to invoke this tool. Schema and curl snippet are visible to anyone.

Schemas

Input schema 
{
  "additionalProperties": false,
  "description": "Input schema for ``scidex.forge.circatlas_circrna``.",
  "properties": {
    "gene_symbol": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Host gene symbol or Ensembl gene ID to query (e.g. 'CDR1AS', 'EGFR'). At least one of gene_symbol or region is required.",
      "title": "Gene Symbol"
    },
    "region": {
      "anyOf": [
        {
          "maxLength": 200,
          "type": "string"
        },
        {
          "type": "null"
        }
      ],
      "default": null,
      "description": "Genomic region in the form 'chr:start-end' or 'chr:start-end:strand' (e.g. 'chr7:1000000-2000000', 'chr17:7565097-7590863'). At least one of gene_symbol or region is required.",
      "title": "Region"
    },
    "limit": {
      "default": 20,
      "description": "Maximum number of circRNA records to return (default 20, max 200).",
      "maximum": 200,
      "minimum": 1,
      "title": "Limit",
      "type": "integer"
    }
  },
  "title": "ForgeCircAtlasCircRNAIn",
  "type": "object"
}
Output schema 
{
  "$defs": {
    "CircRNARecord": {
      "description": "One circular RNA record from circAtlas 3.0.",
      "properties": {
        "circrna_id": {
          "description": "circAtlas stable identifier (e.g. hsa_circ_0001649).",
          "title": "Circrna Id",
          "type": "string"
        },
        "chr": {
          "default": "",
          "description": "Chromosome (e.g. chr7).",
          "title": "Chr",
          "type": "string"
        },
        "start": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "1-based genomic start position.",
          "title": "Start"
        },
        "end": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "1-based genomic end position.",
          "title": "End"
        },
        "strand": {
          "default": "",
          "description": "Genomic strand: '+' or '-'.",
          "title": "Strand",
          "type": "string"
        },
        "gene_symbol": {
          "default": "",
          "description": "Host gene name (e.g. SHPRH, CDR1AS).",
          "title": "Gene Symbol",
          "type": "string"
        },
        "species": {
          "default": "",
          "description": "Species prefix extracted from the circRNA ID (e.g. hsa).",
          "title": "Species",
          "type": "string"
        },
        "tissue_expression": {
          "description": "Tissues or cell types where the circRNA is expressed.",
          "items": {
            "type": "string"
          },
          "title": "Tissue Expression",
          "type": "array"
        },
        "splicing_length": {
          "anyOf": [
            {
              "type": "integer"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Spliced length of the circRNA in nucleotides.",
          "title": "Splicing Length"
        },
        "conservation": {
          "anyOf": [
            {
              "type": "number"
            },
            {
              "type": "null"
            }
          ],
          "default": null,
          "description": "Cross-species conservation score (0–1 where available).",
          "title": "Conservation"
        },
        "mirna_sponge": {
          "description": "miRNA identifiers sponged by this circRNA.",
          "items": {
            "type": "string"
          },
          "title": "Mirna Sponge",
          "type": "array"
        },
        "pmids": {
          "description": "PubMed IDs supporting this circRNA record.",
          "items": {
            "type": "string"
          },
          "title": "Pmids",
          "type": "array"
        }
      },
      "required": [
        "circrna_id"
      ],
      "title": "CircRNARecord",
      "type": "object"
    }
  },
  "description": "Response shape for ``scidex.forge.circatlas_circrna``.",
  "properties": {
    "query": {
      "description": "Human-readable description of the applied query.",
      "title": "Query",
      "type": "string"
    },
    "circrnas": {
      "description": "Matching circular RNA records from circAtlas 3.0.",
      "items": {
        "$ref": "#/$defs/CircRNARecord"
      },
      "title": "Circrnas",
      "type": "array"
    },
    "not_found": {
      "default": false,
      "description": "True when circAtlas returned no records for the given query.",
      "title": "Not Found",
      "type": "boolean"
    },
    "source": {
      "default": "circAtlas 3.0 (ngdc.cncb.ac.cn/circatlas)",
      "description": "Data source identifier.",
      "title": "Source",
      "type": "string"
    },
    "took_ms": {
      "default": 0,
      "description": "Wall-clock time for the upstream API call in milliseconds.",
      "title": "Took Ms",
      "type": "integer"
    }
  },
  "required": [
    "query"
  ],
  "title": "ForgeCircAtlasCircRNAOut",
  "type": "object"
}

curl snippet

Replace $SCIDEX_JWT with a valid bearer token. Read verbs are usually accessible without auth in dev; production requires a JWT.

curl -sS -X POST '/api/scidex/forge/circatlas_circrna' \
  -H 'authorization: Bearer $SCIDEX_JWT' \
  -H 'content-type: application/json' \
  -d '{}'

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